Thursday, November 21, 2013

Is Baker's Yeast a Good Model for the Evolution of Multicellularity?

R. Ford Denison has an excellent blog called This Week in Evolution. He recently posted an article about the evolution of multicellularity [Evolving-multicellularity lab exercises]. That post contains a link to a paper he recently published with a former student (Ratcliff et al., 2013). Here's the abstract.

Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood. Using experimental evolution, we show that key steps in this transition could have occurred quickly. We subjected the unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to be adaptive. We observed the rapid evolution of clustering genotypes that display a novel multicellular life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest. Simple among-cell division of labor rapidly evolved. Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production. These results show that key aspects of multicellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes.

Here's the problem. Most fungi are multicellular and Saccharomyces cerevisiae (budding yeast) almost certainly evolved from an ancestor that could form hyphae. In fact, wild-type diploid strains or Saccharomyces cerevisiae will form multicellular filaments (pseudohypha) in response to starvation for nitrogen (Liu et al., 1996).

Many of the common lab strains have lost the ability to form multicellular pseudohyphae because they carry a nonsense mutation in the FLO8 gene (Liu et al., 1996). Presumably, those strains have been selected by bakers and brewers over the past several thousand years.

In their discussion, Ratcliff et al. (2012) say ...

Although known transitions to complex multicellularity, with clearly differentiated cell types, occurred over millions of years, we have shown that the first crucial steps in the transition from unicellularity to multicellularity can evolve remarkably quickly under appropriate selective conditions.

I don't this this is quite fair since the yeast strain is just reverting to a primitive condition. This might only have required one or a few mutations. It's not a very good model for de novo evolution of multicellarity.

The work from Gerry Fink's lab (e.g. Liu et al. 1996) is a good example of why we should be cautious using yeast as a model for anything. The yeast strains used in the lab have been selected for specific characteristics since bread-making and beer-making were first invented over 4000 years ago. We need to be cautious about drawing general conclusions based on work with lab yeast strains.

The lab exercise based on the Ratcliff et al. (2012) paper [Experimental Evolution of Multicellularity] may be interesting but it's also misleading. The description of that experiment implies that students are reproducing the ancient evolution of multicellularity from single-cell organisms. Instead, what students are actually looking at is the reversion of a derived, exclusively single-cell strain, to the more primitive multicellular state. That's not the same thing.

[Photo Credit: That's Ford at a rally in Ottawa where we were protesting the Conservative government's clamp-down on science in Canada. He took advantage of the audience to advertise his book.

8 comments
:

I seem to remember an old experiment using single algae cells (maybe Chlamydomonas) that formed multicellular structures reminiscent of Volvox (multicellular alga) when challenged by predatory amoebae. Wouldn't that be a better system to study the evolution of multicellularity?

I'm guessing you're referring to this article from 1998, on the algae, Chlorella vulgaris. This article directly addresses Larry's concern that the model organism should have no history of multicellularity. See below.

Abstract: Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.

Since I've written about this research a couple times, I thought it would be useful to provide some comments from the lead author, William Ratcliff, that he left on my blog when similar questions arose:

"Well, I don’t buy it that yeast are multicellular in nature. Certainly some yeast in nature form small clusters (like strain RM11), but as far as I know, these are the exception to the rule. Most strains isolated in nature are unicellular, or at most, flocculating (which I still count as unicellular but social). [CZ: "Flocculating" refers to the clumps that unrelated yeast cells form when they starve.]

In our case, we’re working with strain Y55, a yeast that is is not highly lab adapted (we know this because it still sporulates at nearly 100% efficiency. Sporulation efficiency is typically lost after long periods of lab adaptation.) We’ve known through knockout mutation libraries that breaking the ability to release daughter cells after mitosis gives you a snowflake-shaped cluster. We’re not claiming that we’re the first to observe this phenotype. What we claim is that we’re the first to systematically examine the transition to multicellularity. We see the evolution of clusters from single cells as a result of selection acting on de novo mutations, we see a shift to between-cluster selection, and we see subsequent adaptation occurring cluster-level traits (like division of labor).

Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it. The amazing thing we see is that we rapidly see adaptations to this adaptation. If we select for more rapid settling, snowflake yeast evolve to delay reproduction until the parent is larger, allowing it settle more quickly. We see the evolution of higher rates of apoptosis as a way to regulate the size and number of propagules produced. We show that the transition to multicellularity in yeast is surprisingly easy, and have no reason to suspect it would be any harder in other microbes with a reproductive process similar to yeast."

I don't buy it. The fact is that many yeasts can form hyphae and unless Fink and his group are lying, they have observed strains of Saccharomyces cerevisiae that have multicellular stages.

That means that this is not a good model for the de novo evolution of multicellularity. I suggest that Ratcliff et al. actually try the same experiment with E. coli, paramecium, or diatoms. If they were successful with those species in only a few weeks, it really would be exciting.

Larry--Ratcliff and company have just published a paper where they get multicellularity out of Chladymonas (link below).

From the abstract:

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in ***a unicellular organism that has never had a multicellular ancestor.*** [Emphasis mine--CZ] We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that it did not evolve for this purpose. Instead, we find that unicellular propagules are adaptive even in the absence of intercellular conflict, maximizing cluster-level fecundity. These results demonstrate that the unicellular bottleneck, a trait essential for evolving multicellular complexity, can arise rapidly via co-option of the ancestral unicellular form.

I'm aware of this paper. One out of 20 cultures showed formation of clusters after about 150 days. It's a much better experiment than the yeast experiment. I'm not sure that it deserved as much hype as it got.

I didn't notice that the authors specifically mentioned that the algae was "a unicellular organism that has never had a multicellular ancestor." It shows that the authors recognized the problem with their earlier experiment.

In relation to Larry's concern about model organisms with no history of multicullularity, I posted a reference above to a 1998 paper on evolution of multicellularity by Boraas, Seale, & Boxhorn, on the green algae Chlorella vulgaris.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

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The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

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My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
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Francis Crick
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Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.